tbuckley/cabot-search huggingface dataset:
Dysfunctional dendritic cells limit antigen-specific T cell response in glioma
Authors: Mirco Friedrich, Markus Hahn, Julius Michel, Roman Sankowski, Michael Kilian, Niklas Kehl, Manina Günter, Theresa Bunse, Stefan Pusch, Andreas von Deimling, Wolfgang Wick, Stella E Autenrieth, Marco Prinz, Michael Platten, Lukas Bunse
Journal: Neuro-Oncology (2022)

Abstract Background Dendritic cells (DC), the most potent professional antigen presenting cells capable of effective cross-presentation, have been demonstrated to license T helper cells to induce antitumor immunity in solid tumors. Specific DC subtypes are recruited to the injured brain by microglial chemokines, locally adapting to distinct transcriptional profiles. In isocitrate dehydrogenase (IDH) type 1 mutant gliomas, monocyte-derived macrophages have recently been shown to display an attenuated intratumoral antigen presentation capacity as consequence of the local accumulation of the oncometabolite R-2-hydroxyglutarate. The functionality and the contribution of DC to the IDH-mutant tumor microenvironment (TME) remains unclear. Methods Frequencies and intratumoral phenotypes of human DC in IDH-wildtype (IDHwt) and -mutant high-grade gliomas are comparatively assessed by transcriptomic and proteomic profiling. DC functionality is investigated in experimental murine glioblastomas expressing the model antigen ovalbumin. Single-cell sequencing-based pseudotime analyses and spectral flow cytometric analyses are used to profile DC states longitudinally. Results DC are present in primary and recurrent high-grade gliomas and interact with other immune cell types within the TME. In murine glioblastomas, we find an IDH-status-associated major histocompatibility class I-restricted cross-presentation of tumor antigens by DC specifically in the tumor but not in meninges or secondary lymphoid organs of tumor-bearing animals. In single-cell sequencing-based pseudotime and longitudinal spectral flow cytometric analyses, we demonstrate an IDH-status-dependent differential, exclusively microenvironmental education of DC. Conclusions Glioma-associated DCs are relevantly abundant in human IDHwt and mutant tumors. Glioma IDH mutations result in specifically educated, dysfunctional DCs via paracrine reprogramming of infiltrating monocytes, providing the basis for combinatorial immunotherapy concepts against IDH mutant gliomas.
Abstract 2955: SMYD2 regulates chromatin modifier KMT2D in ER+/PIK3CA mutant breast cancer
Authors: Ryan Blawski, Mirna Sallaku, Xinyu Guo, Srushti Kittane, Maurizio Scaltriti, Minkui Luo, Eneda Toska
Journal: Cancer Research (2022)

Abstract Breast cancer leads current cancer diagnoses worldwide, accounting for 1 in 4 cancer cases and 1 in 6 cancer deaths in women. Over 70% of breast tumors are hormone receptor positive and can be treated with endocrine therapy, however tumor recurrence remains a major obstacle. Oncogenic mutations in the catalytic subunit of PI3K occur in up to 40% of ER+/HER2- negative breast tumors, making it a promising therapeutic target. Clinically, PI3K inhibitors have shown limited efficacy as monotherapy due to a number of resistance mechanisms, including an upregulation of ER-dependent signaling. Identification of the ER-PI3K signaling crosstalk led to clinical trials which resulted in the approval of the PI3K inhibitor alpelisib in combination with fulvestrant in patients with hormone-refractory ER+/PIK3CA-mutant breast cancer. Further work uncovered a key role for the chromatin modifier KMT2D in regulating ER-dependent transcription upon PI3K inhibition. PI3K effectors AKT1/SGK1 negatively regulate KMT2D through direct S1331 phosphorylation. When PI3K is inhibited, this downstream regulatory event is lost, leading to increased chromatin recruitment of KMT2D and an upregulation of ER-dependent transcription. We have identified a novel methylation site on KMT2D, at K1330 directly adjacent to S1331, catalyzed by the lysine methyltransferase SMYD2. Knockdown of SMYD2 sensitizes ER+/PIK3CA mutant breast cancer cell lines to PI3K inhibition. The combination of SMYD2 knockdown and alpelisib leads to a significant reduction in tumor growth compared to alpelisib alone in a xenograft model. Mechanistically, SMYD2 knockdown is able to attenuate alpelisib-induced KMT2D chromatin binding globally and at ER loci. Accordingly, loss of SMYD2 abrogates alpelisib-induced changes in gene expression, including ER-dependent transcription. Altogether our results demonstrate a role for epigenetic therapy using SMYD2 inhibitors in combination with alpelisib for the treatment of ER+/PIK3CA mutant breast cancer. Citation Format: Ryan Blawski, Mirna Sallaku, Xinyu Guo, Srushti Kittane, Maurizio Scaltriti, Minkui Luo, Eneda Toska. SMYD2 regulates chromatin modifier KMT2D in ER+/PIK3CA mutant breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2955.
Abstract 2068: An ADCC enhanced anti-CCR8 antibody, which preferentially depletes tumor regulatory T cells and inhibits tumor growth
Authors: Jamil A. Haque, Cristina Domeier, Paul A. Algate, Zhi Liu, Wei Yan, YuFeng Peng
Journal: Cancer Research (2022)

Abstract Tumor associated FOXP3+ regulatory T cells (Tregs) suppress antitumor immunity, thereby hindering protective immunosurveillance of tumors and hampering effective antitumor immune responses in tumor-bearing hosts. Eliminating the suppressive effects of tumor associated Tregs could, therefore, enhance antitumor activity of existing immunotherapies. CCR8 is a seven transmembrane G-coupled protein whose expression is highly upregulated on tumor associated Tregs in several types of tumors, but not on peripheral Tregs. The specific expression on tumor associated Tregs makes CCR8 an ideal target for treating cancers. The chemokine CCL1 interacts with the N terminus and second extracellular domain of CCR8. CCL1 produced by tumor associated macrophages can induce Tregs migration to the tumors. PSB114, a humanized anti-hCCR8 IgG1 antibody, was developed to block CCL1 mediated Tregs chemotaxis and deplete tumor associated CCR8-expressing Tregs. PSB114 was affinity matured by yeast display and glyco-modified to enhance its ADCC activity. PSB114 has high binding affinity for human CCR8 without significant binding to other membrane proteins, resulting in a favorable PK in hFcRn transgenic mice (T1/2 &amp;gt; 13 days). PSB114 is highly specific for the activated Tregs with low picomolar EC50 of depletion activity. When tested in bioassays, PSB114 enhances T cell activation and TNFα production from activated PBMCs. In a humanized mouse model, PSB114 preferentially depletes tumor infiltrating Tregs and increases NK and CD8 T cell infiltration within the tumor. Moreover, PBS114 significantly inhibited MC38 tumor growth in hCCR8 knock-in mice. These results demonstrate the potential of PSB114 for treating cancers in human. Citation Format: Jamil A. Haque, Cristina Domeier, Paul A. Algate, Zhi Liu, Wei Yan, YuFeng Peng. An ADCC enhanced anti-CCR8 antibody, which preferentially depletes tumor regulatory T cells and inhibits tumor growth [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2068.
Response to “Comment on ‘Evaluation of a Gene–Environment Interaction of <i>PON1</i> and Low-Level Nerve Agent Exposure with Gulf War Illness: A Prevalence Case–Control Study Drawn from the U.S. Military Health Survey’s National Population Sample’”
Authors: Robert W. Haley, Jill A. Dever, John F. Teiber
Journal: Environmental Health Perspectives (2022)
Abstract 3992: Modular ddPCR assay design for highly sensitive single nucleotide variant detection
Authors: Sarah Heine, Ashley Beams, Nathan Riccitelli, Shabnam Tangri
Journal: Cancer Research (2022)

Abstract Introduction: Single-nucleotide variants (SNVs) are key drivers of both oncogenesis and emergent resistance to targeted therapies. Although high-throughput Identification of SNVs can be achieved with Next Generation Sequencing (NGS) technologies, the cost is significant, and proportional to the desired sensitivity of variant detection. Conversely, while only small numbers of SNVs can be queried in an individual quantitative PCR (qPCR) or droplet digital PCR (ddPCR) reaction, a fully optimized qPCR or ddPCR assay can detect SNVs at very low frequencies for a fraction of the cost of sequencing. Herein, we present a generalizable approach to PCR assay design, using a combination of mutation-sensitive induced mismatch primers, wild-type suppressors, and TaqMan probes, that permits detection of SNVs below 0.1%. Method: Known oncogenic hotspot regions were selected for development of mutation-detecting PCR assays. For each hotspot, a mutation-specific-mismatch primer, suppressor, and probe (MSMPSP) cassette was designed consisting of 1) a mutation-bearing forward primer with engineered mismatches, 2) a wild-type, extension-locked blocker oligo, 3) a fluorescent TaqMan probe, and 4) a downstream reverse primer. Designed mutation assays were evaluated using plasmid control sequences, remnant clinical specimens, and healthy donor peripheral blood samples spiked with known quantities of mutation-bearing plasmid or cell lines and processed on the BioRad AutoDG/QX200 droplet digital PCR system. Results: Variant detection below 0.1% was achieved for all tested mutations, including those residing in homopolymeric and GC-rich regions, from as low as 100 ng DNA input, in a single day. At higher variant frequencies accessible to multiple platforms, results with MSMPSP-based ddPCR assays exhibited excellent concordance with NGS and qPCR results and yielded linear signal decline down to 0.01% variant allele frequency. Overall assay sensitivity was proportional to DNA input, and improved detection limits were achieved by increased DNA input and combined well analysis. Conclusion: Utilizing the MSMPSP approach, coupled with ddPCR, variant detection for targeted mutations below 0.1% is achievable in diverse genomic contexts. Furthermore, simple design principles and flexible probe-binding sites permit rapid development of new assays, allowing critical mutations to be tracked as they are discovered. While multiplexing capabilities are reduced compared with NGS, short time-to-results, coupled with low cost-per-sample for MSMPSP ddPCR, permits faster treatment decisions at reduced cost to the healthcare system. Citation Format: Sarah Heine, Ashley Beams, Nathan Riccitelli, Shabnam Tangri. Modular ddPCR assay design for highly sensitive single nucleotide variant detection [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3992.
Abstract 1376: Dysfunctional and tolerant CD8 T cell persistence in premalignant lesions
Authors: Jessica J. Roetman, Megan M. Erwin, Minna K. Apostolova, Mary Philip
Journal: Cancer Research (2022)

Abstract T cells have the potential to carry out potent anti-tumor responses. Most studies examining T cell-cancer interactions have been directed toward late-stage tumors, but much less is known about how T cells respond to premalignant lesions. Using a clinically relevant liver cancer mouse model (Albumin-Stop-Large T Antigen; AST) in which the SV40 Large T Antigen (TAG) serves as oncogene and tumor neoantigen, we previously demonstrated that TAG-specific CD8 T cells (TCR-TAG) rapidly become dysfunctional (unable to produce cytokines and cytolytic molecules) after entering premalignant liver lesions, although they persist long-term. We hypothesized that peripheral tolerance mechanisms, which prevent autoimmunity against self-antigens, drive T cell dysfunction in premalignant lesions. To test this, we compared CD8 T cell (TCR-GAG) responses to a liver self-antigen (GAG) to TCR-TAG responses to the TAG neoantigen in premalignant hepatocytes. We found that liver-reactive TCR-GAG were unable to produce cytokines, similar to neoantigen-specific TCR-TAG; however, in contrast, they failed to persist. To test whether oncogenic transformation of hepatocytes promoted T cell persistence, we crossed Alb-GAG and AST mice to generate a model in which GAG and TAG was expressed in premalignant hepatocytes (ASTxAlb-GAG). We found that both TCR-GAG and TCR-TAG transferred into ASTxAlb-GAG mice bearing premalignant lesions driven by the TAG oncogene rapidly lost the ability to produce cytokines; however, only TCR-TAG persisted while TCR-GAG quickly disappeared. To understand why the TCR-GAG failed to persist, we assessed proliferation and cell cycling after T cells encountered their cognate antigen. While both TCR-GAG and TCR-TAG were rapidly activated and began proliferating, TCR-GAG exited cell cycle and began decreasing in number after four cell divisions, while TCR-TAG continued to divide and increase in number. Antigen amount and localization may regulate T cell proliferation and persistence. We found much higher levels of TAG-encoding versus GAG-encoding mRNA in the liver, suggesting that higher antigen expression may be required for T cell persistence. T cell responses can be directed against both shared tumor self-antigens and neoantigens. By dissecting the determinants of CD8 T cell function and persistence in response to self and non-self-antigens, these studies could inform strategies to boost anti-tumor CD8 T cell responses in cancer patients. Citation Format: Jessica J. Roetman, Megan M. Erwin, Minna K. Apostolova, Mary Philip. Dysfunctional and tolerant CD8 T cell persistence in premalignant lesions [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1376.
Abstract 3376: Novel reference materials for the analysis of methylation in liquid biopsies
Authors: Jayanthi Ramprakash, Matthew G. Butler, Russell K. Garlick, Yves Konigshofer
Journal: Cancer Research (2022)

Abstract Here we describe new reference materials (RMs) for liquid biopsies that are designed to mimic the methylation found in circulating cell-free DNA (ccfDNA). Methylation is an important epigenetic modification that influences cellular differentiation and gene expression. Recently, liquid biopsies have started to incorporate analyses of epigenetic modifications for screening purposes to detect cancer-derived DNA in the blood. Additionally, epigenetic modifications are being used to also assign a tissue of origin to the cancer to direct confirmatory diagnostic procedures. Obtaining sufficient amounts of ccfDNA for assay development, validation, and proficiency testing is difficult. Furthermore, methods of analyzing the epigenetic modifications, such as bisulfite conversion, can damage a significant fraction of the input material; but, failing to carry them out to completion can result in an over-estimation of methylation. To address the challenges associated with assessing the methylation of ccfDNA, we created and characterized three types of RMs. The first type of RM is a fragmented genome of the GM24385 reference cell line that is used to create a set of RMs with different degrees of methylation (0%, ~25%, ~50%, ~75% and close to 100%). The exact degree of methylation was assigned by digital PCR using assays for heterozygous SNPs, where one allele is both a site for CpG methylation and a recognition site for a methylation-sensitive restriction enzyme while the other allele is not. The second type of RM is an amplified ccfDNA sample that has been methylated similarly but also reproduces the fragment lengths and genomic representation biases of ccfDNA. The degree of methylation was assigned by digital PCR, but only a subset of assays was useful because not all SNPs were heterozygous. The third type of RM is an amplified ccfDNA sample that has been processed to mimic the methylation found in the original ccfDNA. Analyses of the RMs by whole genome sequencing (WGS) showed that, while bisulfite conversion and/or the amplification of the resulting dU-containing DNA appeared to lead to significant biases in genomic representation, the resulting data was generally in agreement with the amount of methylation assigned by digital PCR. Additionally, it was possible to prepare an RM that generally reproduces the methylation found in ccfDNA; although, this was limited to individual molecules having either no or close to full methylation, which is unlikely to be the case for all molecules of ccfDNA in vivo. Citation Format: Jayanthi Ramprakash, Matthew G. Butler, Russell K. Garlick, Yves Konigshofer. Novel reference materials for the analysis of methylation in liquid biopsies [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3376.
Abstract 2247: Prostate cancer-related mortality risk assessment in a cohort of southern Nigerian men
Authors: Jude O. Okoye, Vivian I. Ogbonnaya, Chiemeka M. Emeka, Okechi Obioma
Journal: Cancer Research (2022)

Abstract Background: Overexpression of breast cancer susceptibility gene 2 (BRCA2) in patients with prostate cancer is associated with a high Gleason score at diagnosis, poorly differentiated tumors, poor prognosis, and disease recurrence. Such aggressive tumors possess high iron storage which promotes inflammation, angiogenesis, and cell proliferation. Expression of iron progressively increases with cancer grade and stage. Purpose: This study evaluated the expression of BRCA2 protein and Iron expression in Gleason’s graded prostate cancer tissues, in a bid to determine the disease aggressiveness and mortality risk among Southern Nigerian men. Methods: In this retrospective study, 86 formalin-fixed paraffin-embedded prostate cancer tissues (diagnosed in 2018 and 2019) were reviewed using Gleason’s grading system. Tissues stained for iron and BRCA2 proteins using histochemical and immunohistochemical staining techniques, respectively. Staining intensity was scored using a scale of 0, +1, +2, and +3. For BRCA2 and Iron expressions, score 0 and +1 were considered negative while score +2 and +3 were considered positive. Pearson’s chi-square test was used to determine the association between Gleason’s grade and expression of BRCA2 and iron. Results: The prevalence of prostate cancer in the age groups of 50-59, 60-69, 70-79, 80-89, and 90-99 years was 10.8%, 32.4%, 40.5%, 13.5% and 2.7%, respectively. Using the Gleason’s grading pattern, the frequency of Grade (mean age in years) I, II, III, IV and V was 9.3% (70.25 ± 6.95), 16.3% (77.29 ± 6.23), 16.3% (75.57 ± 12.59), 25.6% (72.75 ± 7.80) and 32.6% (67.42 ± 9.76), respectively. Higher frequency of BRCA2 and Iron expression were observed in ≥G4 (37.5% and 72.7%) than in ≤G3 (versus 16.7% and 11.8%) at p= 0.191 and p&amp;lt; 0.001, respectively. The prevalence of BRCA2 negative and positive tissues was 65.1% and 34.9%, respectively whereas the prevalence of iron negative and positive tissues was 48.7% and 51.3%, respectively. There was an inverse relationship between tumour grade and age (p= 0.108), and direct relationships between tumour grade and BRCA2 (p= 0.059), tumour grade and iron (p= 0.000), BRCA2 and Iron expressions (p= 0.027), BRCA2 expression and age (p= 0.019), and Iron and age (p= 0.281). Patients with prostate cancer who are within the age group of 50-59 years and those with ≥G4 require close monitoring for improved survival. Conclusion: This study revealed a high prevalence of aggressive prostate cancer and suggests that there is a high mortality risk among Southern Nigerian men diagnosed with the disease. Citation Format: Jude O. Okoye, Vivian I. Ogbonnaya, Chiemeka M. Emeka, Okechi Obioma. Prostate cancer-related mortality risk assessment in a cohort of southern Nigerian men [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2247.
Abstract 2538: Role of <i>Argonaute</i> 2 in regulation of immune microenvironment in pancreatic cancer
Authors: Jennifer Hon, Carson Kenum, Pushpinder S. Bawa, Vijaya L. Dommeti, Anastasia A. Sahu, Miriam Gandham, Chi-Chiang Li, Zainab I. Taher, Sylvia Zelenka-Wang, Jean C. Tien, Sunita Shankar, Seema Chugh, Arul M. Chinnaiyan
Journal: Cancer Research (2022)

Abstract KRAS mutations have been observed in nearly 95% of pancreatic ductal adenocarcinoma (PDAC), however targeting KRAS remains a major therapeutic challenge. Previous studies from our group have discovered a novel interaction between KRAS and Argonaute 2 (AGO2) and have uncovered a significant role of this interaction in regulating KRAS signaling. Knockout of AGO2 in genetically engineered mouse models of KRAS driven pancreatic and lung cancer dramatically impacted tumor progression. Intriguingly, in pancreatic cancer loss of AGO2 expression resulted in early pancreatic intraepithelial lesions (PanINs) that failed to progress to PDAC. We observed increased senescence in these AGO2 knockout lesions that abrogated PDAC progression. Further, there was pronounced infiltration of immune cells in pancreata lacking AGO2 in comparison to wild type. We particularly observed a 20-fold increase in natural killer (NK) cells population in pancreata lacking AGO2. This instigated us to evaluate potential role of AGO2 in regulating immune microenvironment in pancreatic cancer. Gene set enrichment analysis of AGO2 knockout SW1990 PDAC cells revealed significant upregulation of inflammatory and interferon response pathways. We observed increased expression of several signaling proteins implicated in immune activation pathways. Further characterization of these knockout cells indicated upregulation of MHC proteins that consequently added to mechanistic insights. Additionally, we are also exploring syngeneic models of pancreatic cancer and we will present findings from our ongoing studies to evaluate the impact of AGO2 knockout on immune axis. Overall, our findings suggest potential involvement of AGO2 in regulating immune microenvironment in pancreatic cancer. Citation Format: Jennifer Hon, Carson Kenum, Pushpinder S. Bawa, Vijaya L. Dommeti, Anastasia A. Sahu, Miriam Gandham, Chi-Chiang Li, Zainab I. Taher, Sylvia Zelenka-Wang, Jean C. Tien, Sunita Shankar, Seema Chugh, Arul M. Chinnaiyan. Role of Argonaute 2 in regulation of immune microenvironment in pancreatic cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2538.